We compare three models: * Binomial (B) * Beta-Binomial (BB) * Zero-inflated Beta-Binomial (ZIBB)
See vignette ‘ModelOverview’ to inspect the different models.
FALSE
FALSE Computed from 4000 by 2001 log-likelihood matrix
FALSE
FALSE Estimate SE
FALSE elpd_loo -5885.3 82.5
FALSE p_loo 1309.2 27.5
FALSE looic 11770.6 165.0
FALSE ------
FALSE Monte Carlo SE of elpd_loo is NA.
FALSE
FALSE Pareto k diagnostic values:
FALSE Count Pct. Min. n_eff
FALSE (-Inf, 0.5] (good) 511 25.5% 248
FALSE (0.5, 0.7] (ok) 311 15.5% 85
FALSE (0.7, 1] (bad) 901 45.0% 19
FALSE (1, Inf) (very bad) 278 13.9% 3
FALSE See help('pareto-k-diagnostic') for details.
FALSE
FALSE Computed from 4000 by 2001 log-likelihood matrix
FALSE
FALSE Estimate SE
FALSE elpd_loo -6903.7 103.1
FALSE p_loo 356.2 19.0
FALSE looic 13807.4 206.2
FALSE ------
FALSE Monte Carlo SE of elpd_loo is NA.
FALSE
FALSE Pareto k diagnostic values:
FALSE Count Pct. Min. n_eff
FALSE (-Inf, 0.5] (good) 1683 84.1% 502
FALSE (0.5, 0.7] (ok) 246 12.3% 111
FALSE (0.7, 1] (bad) 68 3.4% 28
FALSE (1, Inf) (very bad) 4 0.2% 4
FALSE See help('pareto-k-diagnostic') for details.
FALSE
FALSE Computed from 4000 by 2001 log-likelihood matrix
FALSE
FALSE Estimate SE
FALSE elpd_loo -6686.3 101.9
FALSE p_loo 527.4 24.1
FALSE looic 13372.6 203.7
FALSE ------
FALSE Monte Carlo SE of elpd_loo is NA.
FALSE
FALSE Pareto k diagnostic values:
FALSE Count Pct. Min. n_eff
FALSE (-Inf, 0.5] (good) 1382 69.1% 370
FALSE (0.5, 0.7] (ok) 396 19.8% 117
FALSE (0.7, 1] (bad) 202 10.1% 21
FALSE (1, Inf) (very bad) 21 1.0% 2
FALSE See help('pareto-k-diagnostic') for details.
FALSE elpd_diff se_diff elpd_loo
FALSE loo::loo(loo::extract_log_lik(B$glm)) 0.0 0.0 -5885.3
FALSE loo::loo(loo::extract_log_lik(ZIBB$glm)) -801.0 46.5 -6686.3
FALSE loo::loo(loo::extract_log_lik(BB$glm)) -1018.4 35.9 -6903.7
FALSE p_loo looic
FALSE loo::loo(loo::extract_log_lik(B$glm)) 1309.2 11770.6
FALSE loo::loo(loo::extract_log_lik(ZIBB$glm)) 527.4 13372.6
FALSE loo::loo(loo::extract_log_lik(BB$glm)) 356.2 13807.4
Comparisons:
Five genes for which the pairwise models inferred most discrepant usage coefficients are annotated.